Variant report

Variant	rs4646285
Chromosome Location	chr14:70263648-70263649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:70261200..70263802-chr14:70264379..70267059,2	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10130926	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10136397	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10136529	0.81[ASN][1000 genomes]
rs10142027	0.87[ASN][1000 genomes]
rs10142031	0.87[ASN][1000 genomes]
rs10143223	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs10146537	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10148404	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10151895	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs10459536	0.89[ASN][1000 genomes]
rs11620808	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11621916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11622580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11622925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623262	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11624523	0.90[CHB][hapmap];0.96[CHD][hapmap];0.89[ASN][1000 genomes]
rs11624532	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11625731	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11625932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11626145	0.86[EUR][1000 genomes]
rs11627012	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11627089	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11628423	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11628546	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11628665	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11629054	0.92[CHD][hapmap]
rs12431573	0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13313365	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13313366	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13313388	0.81[ASN][1000 genomes]
rs14411	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17328	0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1953399	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1953400	0.88[ASN][1000 genomes]
rs2148503	0.89[ASN][1000 genomes]
rs2148505	0.86[ASN][1000 genomes]
rs2332167	0.90[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs28404963	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28437671	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28437822	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28480224	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2877595	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2877598	0.84[ASN][1000 genomes]
rs28785205	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28847646	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3104	0.90[CHB][hapmap];0.96[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs3784152	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs3784153	0.90[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs3809399	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4646286	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4646297	0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs4899311	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4899313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902753	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902755	0.89[ASN][1000 genomes]
rs4902756	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4902757	0.87[ASN][1000 genomes]
rs55724465	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55987626	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56074637	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56140822	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56177148	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57492222	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58582364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59066042	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59172911	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60442313	0.89[ASN][1000 genomes]
rs61356864	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6573905	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6573906	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6573907	0.85[ASN][1000 genomes]
rs6573908	0.90[CHB][hapmap];0.96[CHD][hapmap];0.84[ASN][1000 genomes]
rs6573909	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7142868	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs7153496	0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs7153985	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7154439	0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7160953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7161476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72725718	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72725724	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72725740	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72725743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72725745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72725773	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72725776	0.89[EUR][1000 genomes]
rs72725780	0.89[EUR][1000 genomes]
rs8005609	0.82[ASN][1000 genomes]
rs8010836	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8011311	0.92[ASN][1000 genomes]
rs8013598	0.85[ASN][1000 genomes]
rs8014236	0.83[ASN][1000 genomes]
rs8021735	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9944036	0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4646285	TTC9	cis	parietal	SCAN
rs4646285	SLC8A3	cis	parietal	SCAN
rs4646285	PSMC3	trans	cerebellum	SCAN
rs4646285	ERH	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70246400-70264000	Weak transcription	Fetal Intestine Small	intestine
2	chr14:70247000-70264600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr14:70248200-70271600	Weak transcription	Psoas Muscle	Psoas
4	chr14:70248400-70264400	Weak transcription	Esophagus	oesophagus
5	chr14:70248800-70264000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr14:70249000-70264000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr14:70251800-70264200	Weak transcription	Colonic Mucosa	Colon
8	chr14:70253400-70263800	Weak transcription	Brain Anterior Caudate	brain
9	chr14:70253400-70264200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr14:70253600-70263800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr14:70253600-70263800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr14:70253800-70264000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr14:70254200-70265800	Weak transcription	Spleen	Spleen
14	chr14:70254800-70275600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:70262000-70264000	Active TSS	Liver	Liver
16	chr14:70262600-70264200	Enhancers	HepG2	liver
17	chr14:70263000-70263800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr14:70263400-70264400	Enhancers	Left Ventricle	heart
19	chr14:70263400-70264400	Enhancers	Right Atrium	heart
20	chr14:70263400-70264800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr14:70263400-70265000	Enhancers	Fetal Intestine Large	intestine
22	chr14:70263400-70265000	Enhancers	Lung	lung
23	chr14:70263400-70265400	Enhancers	Placenta	Placenta
24	chr14:70263600-70264000	Enhancers	Gastric	stomach
25	chr14:70263600-70264000	Enhancers	Right Ventricle	heart
26	chr14:70263600-70265000	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr14:70263600-70265200	Enhancers	Stomach Mucosa	stomach

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